Molecular evolution of ribosomal DNA and its transposons in Daphnia.

大部分植物和动物基因组由影响基因表达模式、细胞分裂速率和细胞大小的重复序列组成。这些重复的或多基因家族的成员在物种之间分化，但在物种内通常是同质的，这被称为协同进化。这种同质性是通过重复单位之间的重组来维持的，其产物在种群水平上受到遗传漂变、基因流动和自然选择的影响。新变异在基因家族和整个物种中传播的速度取决于重组的速度、基因家族的大小、基因家族发生的染色体数量和种群结构。本研究的长期目标是以水蚤的核糖体DNA为模型系统，了解多基因家族进化的机制和结果。 核糖体DNA（rDNA）是一个多基因家族，其RNA产物形成核糖体的组成部分，核糖体是细胞蛋白质合成的位点。核糖体由核糖体RNA（rRNA）和蛋白质组成，rRNA执行催化功能。 在植物和动物中，rDNA由一条或多条染色体上数百至数千个重复单元的串联阵列组成。 植物和动物的rDNA拷贝数比它们产生rRNA所需的要多得多，而且在任何时候只有一部分基因是活跃的。即便如此，rDNA拷贝数的变化可以对大量基因的表达产生实质性影响，因此有可能促成自然选择所能作用的形态和生理变异。 尽管rDNA的重要性，我们仍然不了解它的拷贝数的进化。拟议的研究将通过测试从目前关于rDNA进化的假设中得出的预测来解决这一知识的空白。 我在未来五年的目标是测试以下预测：（1）rDNA中的重组率与rDNA拷贝数呈正相关，（2）rRNA基因的快速进化区域增加了与之相互作用的核糖体蛋白的进化率，以及（3）靶向rDNA的特定区域但也出现在rDNA外部的转座子的分布和拷贝数是它们的相对比率的函数，转座和rDNA重组的速率。 我希望这些结果通过对分子遗传学和进化的基础知识的贡献而引起普遍的兴趣。

A large fraction of plant and animal genomes consists of repeated sequences that impact patterns of gene expression, rates of cell division and cell size. The members of these repeated, or multigene families diverge between species, but are generally homogeneous within species, which is known as concerted evolution. This homogeneity is maintained by recombination between repeat units, the products of which are subject to genetic drift, gene flow and natural selection at the population level. The rate at which new variants spread through a gene family, and an entire species depends on rates of recombination, gene family size, the number of chromosomes on which the gene family occurs and population structure. The long-term goal of my research is to understand the mechanisms and consequences of multigene family evolution using ribosomal DNA in the waterflea, Daphnia as a model system. Ribosomal DNA (rDNA) is a multigene family whose RNA products form an integral component of ribosomes, the site of cellular protein synthesis. Ribosomes are composed of ribosomal RNA (rRNA) and protein, and the rRNA performs the catalytic functions. In plants and animals, rDNA consists of a tandem array of hundreds to thousands of repeat units on one or more chromosomes. Plants and animals have many more rDNA copies than they need to produce rRNA, and only a subset of genes is active at any one time. Even so, changes in rDNA copy number can have substantial effects on the expression of large numbers of genes, and thus has the potential to contribute to morphological and physiological variation on which natural selection can act. Despite the importance of rDNA, there is still much we do not understand about the evolution of its copy number. The proposed research will address gaps in this knowledge by testing predictions derived from current hypotheses on the evolution of rDNA. My goals over the next 5 years are to test the following predictions: (1) rates of recombination in rDNA are positively correlated with rDNA copy number, (2) rapidly-evolving regions of rRNA genes increase the rate of evolution of the ribosomal proteins with which they interact, and (3) the distribution and copy number of transposons that target a specific region of rDNA but also occur outside rDNA is a function of their relative rates of transposition, and the rate of rDNA recombination. I expect the results to be of general interest through their contribution to basic knowledge in molecular genetics and evolution.